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Title: Biodegradation of alkaline lignin by Bacillus ligniniphilus L1

Abstract

Background: Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability to survive in extreme environments. Results: To investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC-MS analyze was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis were carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least 2-fold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABCmore » transport system, environmental response factors, protein synthesis and assembly, etc. Conclusions: GC-MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.« less

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1355089
Report Number(s):
PNNL-SA-124233
Journal ID: ISSN 1754-6834; 48247
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Zhu, Daochen, Zhang, Peipei, Xie, Changxiao, Zhang, Weimin, Sun, Jianzhong, Qian, Wei-Jun, and Yang, Bin. Biodegradation of alkaline lignin by Bacillus ligniniphilus L1. United States: N. p., 2017. Web. doi:10.1186/s13068-017-0735-y.
Zhu, Daochen, Zhang, Peipei, Xie, Changxiao, Zhang, Weimin, Sun, Jianzhong, Qian, Wei-Jun, & Yang, Bin. Biodegradation of alkaline lignin by Bacillus ligniniphilus L1. United States. doi:10.1186/s13068-017-0735-y.
Zhu, Daochen, Zhang, Peipei, Xie, Changxiao, Zhang, Weimin, Sun, Jianzhong, Qian, Wei-Jun, and Yang, Bin. Tue . "Biodegradation of alkaline lignin by Bacillus ligniniphilus L1". United States. doi:10.1186/s13068-017-0735-y.
@article{osti_1355089,
title = {Biodegradation of alkaline lignin by Bacillus ligniniphilus L1},
author = {Zhu, Daochen and Zhang, Peipei and Xie, Changxiao and Zhang, Weimin and Sun, Jianzhong and Qian, Wei-Jun and Yang, Bin},
abstractNote = {Background: Lignin is the most abundant aromatic biopolymer in the biosphere and it comprises up to 30% of plant biomass. Although lignin is the most recalcitrant component of the plant cell wall, still there are microorganisms able to decompose it or degrade it. Fungi are recognized as the most widely used microbes for lignin degradation. However, bacteria have also been known to be able to utilize lignin as a carbon or energy source. Bacillus ligniniphilus L1 was selected in this study due to its capability to utilize alkaline lignin as a single carbon or energy source and its excellent ability to survive in extreme environments. Results: To investigate the aromatic metabolites of strain L1 decomposing alkaline lignin, GC-MS analyze was performed and fifteen single phenol ring aromatic compounds were identified. The dominant absorption peak included phenylacetic acid, 4-hydroxy-benzoicacid, and vanillic acid with the highest proportion of metabolites resulting in 42%. Comparison proteomic analysis were carried out for further study showed that approximately 1447 kinds of proteins were produced, 141 of which were at least 2-fold up-regulated with alkaline lignin as the single carbon source. The up-regulated proteins contents different categories in the biological functions of protein including lignin degradation, ABC transport system, environmental response factors, protein synthesis and assembly, etc. Conclusions: GC-MS analysis showed that alkaline lignin degradation of strain L1 produced 15 kinds of aromatic compounds. Comparison proteomic data and metabolic analysis showed that to ensure the degradation of lignin and growth of strain L1, multiple aspects of cells metabolism including transporter, environmental response factors, and protein synthesis were enhanced. Based on genome and proteomic analysis, at least four kinds of lignin degradation pathway might be present in strain L1, including a Gentisate pathway, the benzoic acid pathway and the β-ketoadipate pathway. The study provides an important basis for lignin degradation by bacteria.},
doi = {10.1186/s13068-017-0735-y},
journal = {Biotechnology for Biofuels},
issn = {1754-6834},
number = 1,
volume = 10,
place = {United States},
year = {2017},
month = {2}
}

Works referenced in this record:

Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation
journal, July 2015

  • Rashid, Goran M. M.; Taylor, Charles R.; Liu, Yangqingxue
  • ACS Chemical Biology, Vol. 10, Issue 10
  • DOI: 10.1021/acschembio.5b00298

Flagella and bacterial pathogenicity: Flagella and bacterial pathogenicity
journal, February 2012

  • Duan, Qiangde; Zhou, Mingxu; Zhu, Liqian
  • Journal of Basic Microbiology, Vol. 53, Issue 1
  • DOI: 10.1002/jobm.201100335

Optimization for peptide sample preparation for urine peptidomics
journal, January 2014

  • Sigdel, Tara K.; Nicora, Carrie D.; Hsieh, Szu-Chuan
  • Clinical Proteomics, Vol. 11, Issue 1
  • DOI: 10.1186/1559-0275-11-7

Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation
journal, July 2013

  • Yakovlev, Igor A.; Hietala, Ari M.; Courty, Pierre-Emmanuel
  • Fungal Genetics and Biology, Vol. 56
  • DOI: 10.1016/j.fgb.2013.04.011

Identification of low molecular weight aromatic compounds by gas chromatography–mass spectrometry (GC–MS) from kraft lignin degradation by three Bacillus sp.
journal, June 2007

  • Raj, Abhay; Krishna Reddy, M. M.; Chandra, Ram
  • International Biodeterioration & Biodegradation, Vol. 59, Issue 4
  • DOI: 10.1016/j.ibiod.2006.09.006

Depolymerization and decolorization of kraft lignin by bacterium Comamonas sp. B-9
journal, August 2013

  • Chai, Li-yuan; Chen, Yue-hui; Tang, Chong-jian
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 4
  • DOI: 10.1007/s00253-013-5166-5

Decolorization of kraft pulp bleaching effluent by a newly isolated fungus,Geotrichum candidum Dec 1
journal, October 2002

  • Shintani, Noboru; Sugano, Yasushi; Shoda, Makoto
  • Journal of Wood Science, Vol. 48, Issue 5
  • DOI: 10.1007/BF00770700

Lignin oxidation and depolymerisation in ionic liquids
journal, January 2016

  • Prado, R.; Brandt, A.; Erdocia, X.
  • Green Chemistry, Vol. 18, Issue 3
  • DOI: 10.1039/C5GC01950H

Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens: Benzoate metabolism in G. metallireducens
journal, October 2005


High activity catechol 1,2-dioxygenase from Stenotrophomonas maltophilia strain KB2 as a useful tool in cis,cis-muconic acid production
journal, March 2013

  • Guzik, Urszula; Hupert-Kocurek, Katarzyna; Sitnik, Małgorzata
  • Antonie van Leeuwenhoek, Vol. 103, Issue 6
  • DOI: 10.1007/s10482-013-9910-8

P450 monooxygenases (P450ome) of the model white rot fungus Phanerochaete chrysosporium
journal, March 2012


A cloned Bacillus halodurans multicopper oxidase exhibiting alkaline laccase activity
journal, February 2004


Catalytic Lignin Valorization Process for the Production of Aromatic Chemicals and Hydrogen
journal, June 2012

  • Zakzeski, Joseph; Jongerius, Anna L.; Bruijnincx, Pieter C. A.
  • ChemSusChem, Vol. 5, Issue 8
  • DOI: 10.1002/cssc.201100699

Identification and Characterization of a Multifunctional Dye Peroxidase from a Lignin-Reactive Bacterium
journal, September 2012

  • Brown, Margaret E.; Barros, Tiago; Chang, Michelle C. Y.
  • ACS Chemical Biology, Vol. 7, Issue 12
  • DOI: 10.1021/cb300383y

Discovery and Characterization of Heme Enzymes from Unsequenced Bacteria: Application to Microbial Lignin Degradation
journal, November 2011

  • Brown, Margaret E.; Walker, Mark C.; Nakashige, Toshiki G.
  • Journal of the American Chemical Society, Vol. 133, Issue 45
  • DOI: 10.1021/ja203972q

Enzymatic "Combustion": The Microbial Degradation of Lignin
journal, October 1987


Detecting differential protein expression in large-scale population proteomics
journal, June 2014


Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea
journal, February 2014

  • Zhu, D.; Tanabe, S. -H.; Xie, C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5
  • DOI: 10.1099/ijs.0.058610-0

Identification of Three Alcohol Dehydrogenase Genes Involved in the Stereospecific Catabolism of Arylglycerol- -Aryl Ether by Sphingobium sp. Strain SYK-6
journal, June 2009

  • Sato, Y.; Moriuchi, H.; Hishiyama, S.
  • Applied and Environmental Microbiology, Vol. 75, Issue 16
  • DOI: 10.1128/AEM.00880-09

Biogenesis and functions of bacterial S-layers
journal, February 2014

  • Fagan, Robert P.; Fairweather, Neil F.
  • Nature Reviews Microbiology, Vol. 12, Issue 3
  • DOI: 10.1038/nrmicro3213

Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels
journal, June 2014


Degradation of dimeric lignin model compounds by aerobic bacteria isolated from the hindgut of xylophagous termites
journal, January 1997


Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: CYTOCHROME P450 FUNCTIONALITY WITH BENEFITS
journal, October 2013

  • Piontek, Klaus; Strittmatter, Eric; Ullrich, René
  • Journal of Biological Chemistry, Vol. 288, Issue 48
  • DOI: 10.1074/jbc.M113.514521

Improvement in efficiency of lignin degradation by Fenton reaction using synergistic catalytic action
journal, December 2015


CotA of Bacillus subtilis Is a Copper-Dependent Laccase
journal, September 2001


Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
journal, January 2013

  • DeAngelis, Kristen M.; Sharma, Deepak; Varney, Rebecca
  • Frontiers in Microbiology, Vol. 4
  • DOI: 10.3389/fmicb.2013.00280

Fungal aryl-alcohol oxidase: a peroxide-producing flavoenzyme involved in lignin degradation
journal, January 2012

  • Hernández-Ortega, Aitor; Ferreira, Patricia; Martínez, Angel T.
  • Applied Microbiology and Biotechnology, Vol. 93, Issue 4
  • DOI: 10.1007/s00253-011-3836-8

Roles of Small Laccases from Streptomyces in Lignin Degradation
journal, June 2014

  • Majumdar, Sudipta; Lukk, Tiit; Solbiati, Jose O.
  • Biochemistry, Vol. 53, Issue 24
  • DOI: 10.1021/bi500285t

Vanillin Production from Lignin and Its Use as a Renewable Chemical
journal, December 2015

  • Fache, Maxence; Boutevin, Bernard; Caillol, Sylvain
  • ACS Sustainable Chemistry & Engineering, Vol. 4, Issue 1
  • DOI: 10.1021/acssuschemeng.5b01344

The emerging role for bacteria in lignin degradation and bio-product formation
journal, June 2011

  • Bugg, Timothy DH; Ahmad, Mark; Hardiman, Elizabeth M.
  • Current Opinion in Biotechnology, Vol. 22, Issue 3
  • DOI: 10.1016/j.copbio.2010.10.009

Cloning and characterization of a new laccase from Bacillus licheniformis catalyzing dimerization of phenolic acids
journal, March 2008

  • Koschorreck, Katja; Richter, Sven M.; Ene, Augusta B.
  • Applied Microbiology and Biotechnology, Vol. 79, Issue 2
  • DOI: 10.1007/s00253-008-1417-2

Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders
journal, January 2010

  • Ahmad, Mark; Taylor, Charles R.; Pink, David
  • Molecular BioSystems, Vol. 6, Issue 5
  • DOI: 10.1039/b908966g

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
journal, June 2012


Genetic and biochemical characterization of a 4-hydroxybenzoate hydroxylase from Corynebacterium glutamicum
journal, December 2007

  • Huang, Yan; Zhao, Ke-xin; Shen, Xi-Hui
  • Applied Microbiology and Biotechnology, Vol. 78, Issue 1
  • DOI: 10.1007/s00253-007-1286-0

The Catalytic Valorization of Lignin for the Production of Renewable Chemicals
journal, June 2010

  • Zakzeski, Joseph; Bruijnincx, Pieter C. A.; Jongerius, Anna L.
  • Chemical Reviews, Vol. 110, Issue 6, p. 3552-3599
  • DOI: 10.1021/cr900354u

Breaking Down Lignin to High-Value Chemicals: The Conversion of Lignocellulose to Vanillin in a Gene Deletion Mutant of Rhodococcus jostii RHA1
journal, August 2013

  • Sainsbury, Paul D.; Hardiman, Elizabeth M.; Ahmad, Mark
  • ACS Chemical Biology, Vol. 8, Issue 10
  • DOI: 10.1021/cb400505a

Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis:  The Human Proteome
journal, February 2005

  • Qian, Wei-Jun; Liu, Tao; Monroe, Matthew E.
  • Journal of Proteome Research, Vol. 4, Issue 1
  • DOI: 10.1021/pr0498638

Biotechnological opportunities with the β-ketoadipate pathway
journal, December 2012


Global Analysis of the Regulon of the Transcriptional Repressor LexA, a Key Component of SOS Response in Mycobacterium tuberculosis
journal, April 2012

  • Smollett, Katherine L.; Smith, Kimberley M.; Kahramanoglou, Christina
  • Journal of Biological Chemistry, Vol. 287, Issue 26
  • DOI: 10.1074/jbc.M112.357715

Effect of oxidized leachate on degradation of lignin by sulfate-reducing bacteria
journal, May 2009


Vanillin oligomerization as a model of side reactions in lignin fragmentation
journal, July 2012


Stimulation of Mn peroxidase activity: a possible role for oxalate in lignin biodegradation.
journal, February 1993

  • Kuan, I. C.; Tien, M.
  • Proceedings of the National Academy of Sciences, Vol. 90, Issue 4
  • DOI: 10.1073/pnas.90.4.1242

Structure-based Insights into the Catalytic Power and Conformational Dexterity of Peroxiredoxins
journal, August 2011

  • Hall, Andrea; Nelson, Kimberly; Poole, Leslie B.
  • Antioxidants & Redox Signaling, Vol. 15, Issue 3
  • DOI: 10.1089/ars.2010.3624

Photodegradation of lignin from black liquor using a UV/TiO2 system
journal, January 2003


Bioconversion of lignin model compounds with oleaginous Rhodococci
journal, December 2011


Crystal structure of a ferredoxin reductase for the CYP199A2 system from Rhodopseudomonas palustris
journal, December 2009

  • Xu, Feng; Bell, Stephen G.; Peng, Ying
  • Proteins: Structure, Function, and Bioinformatics, Vol. 77, Issue 4
  • DOI: 10.1002/prot.22510

Lignin degradation by selected fungal species
journal, June 2013


Lignin Solubilization and Aqueous Phase Reforming for the Production of Aromatic Chemicals and Hydrogen
journal, January 2011


Differential Expression in Phanerochaete chrysosporium of Membrane-Associated Proteins Relevant to Lignin Degradation
journal, October 2008

  • Shary, S.; Kapich, A. N.; Panisko, E. A.
  • Applied and Environmental Microbiology, Vol. 74, Issue 23
  • DOI: 10.1128/AEM.01997-08

2-Cys peroxiredoxin function in intracellular signal transduction: therapeutic implications
journal, December 2005


Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase
journal, December 2000

  • Senda, Toshiya; Yamada, Takahiro; Sakurai, Nobuyuki
  • Journal of Molecular Biology, Vol. 304, Issue 3
  • DOI: 10.1006/jmbi.2000.4200

    Works referencing / citing this record:

    Biodegradation of alkaline lignin by Bacillus ligniniphilus L1
    other, February 2017